A new paper in the journal Science titled "Homoplasy: From Detecting Pattern to Determining Process and Mechanism of Evolution" admits that it is "contrary to expectations" of evolutionary thinking that "similarity evolves in unrelated taxa." A Physorg article about the paper explains that there are two types of homoplasy: "Parallelism/convergence homoplasy occurs when the same trait is present in two lineages that lack a recent common ancestor. Reversal homoplasy occurs when a trait is present in an ancestor but not its immediate descendants; but appears later in a subsequent descendant." The Science paper itself explains how homoplasy is essentially the opposite of homology:

Homology is what is perceived as the same trait in different taxa and is a true representation of inheritance and phylogeny at the organismal level (e.g., it is the perceived phenotype, not the processes responsible for generating it). Homoplasy is the diametric opposite of homology--underlying similarity that does not result from inheritance at the hierarchical level (e.g., gene, tissue, organ; developmental pattern) being considered.

When evolutionary scientists construct phylogenetic trees, they usually assume that similarity results from inheritance from a common ancestor--homology. But homoplasy throws that assumption into chaos. Because homoplasy represents a similarity that does not result from common ancestry, the Science paper notes that "homoplasy historically posed problems for phylogeneticists."

One pattern that has been particularly difficult for evolutionists to explain is what the paper calls "deep homology." This is found when, as the paper puts it, "Common developmental genetic mechanisms have been shown to underlie features that long were considered classic examples of convergent evolution." Two striking examples are discussed in the paper:

The paired appendages of tetrapods (e.g., salamanders, lizards, mammals) and arthropods (e.g., flies, lobsters, spiders) evolved independently, but integration of phylogenetics, development, and genetics in a hierarchical context shows that homologous gene clusters sharing ancient common ancestry are responsible for the initial outgrowths from the body that become patterned along body axes (front to back, top to bottom, etc.)

The image-forming eyes of invertebrate and vertebrate taxa are convergent organs that share some core developmental genetic mechanisms that exemplify deep homology.

In other words, diverse organisms use the same genes to govern development of limbs and eyes, even though their supposed common ancestors are not thought to have had a common type of limb or eye. What the paper calls "integration of phylogenetics" really means that the genetic traits were far too similar for them to allow that they evolved independently--even though everything else about the phylogeny suggested they had.

This poses a real problem for Darwinian evolution because it means that on the one hand a trait appears to be entirely convergent, but on the other hand virtually identical genetic mechanisms are being used to generate the trait. They call it "deep homology" because it's extremely unlikely that such a high degree of genetic similarity would appear by chance. Since they are inextricably wedded to material causes, they conclude that the similarity must exist due to common ancestry. However, the traits also cannot possibly be entirely homologous since the traits produced by the genes are not found in the common ancestor. Either way, this data shows that at some level, extremely high patterns of biological similarity appeared independently.

As a way out, the paper suggests that genes or suites of genes may be repeatedly "co-opted" in different taxa to perform the same functions independently. This almost sounds like organisms are pre-adapted to evolve a particular trait. In fact, when struggling to explain this data, Ernst Mayr called this phenomenon "hidden potentials of the genotype."

The problem now is that in a Darwinian world, evolution is supposed to be blind to future needs. This kind of data almost sounds like evolution is being directed to evolve the same complex trait over and over again. That doesn't fit with unguided Darwinian processes.

So what other mechanisms can generate identical complex informational patterns in independent taxa without absolutely requiring common inheritance? Paul Nelson and Jonathan Wells answer that question:

An intelligent cause may reuse or redeploy the same module in different systems, without there necessarily being any material or physical connection between those systems. Even more simply, intelligent causes can generate identical patterns independently.

(Paul Nelson and Jonathan Wells, "Homology in Biology," in Darwinism, Design, and Public Education, p. 316 (Michigan State University Press, 2003).)

There is a mechanism that can generate complex sequences of code independently. It's called intelligence.